full wwpdb x-ray structure validation report i · • molecule 4 is dodecyl-beta-d-maltoside...

Full wwPDB X-ray Structure Validation Report iO

Jun 7, 2020 � 12:27 am BST

PDB ID : 3HYWTitle : 3-D X-Ray structure of the sul�de:quinone oxidoreductase of the hyperther-

mophilic bacterium Aquifex aeolicus in complex with decylubiquinoneAuthors : Marcia, M.; Ermler, U.; Peng, G.H.; Michel, H.

Deposited on : 2009-06-23Resolution : 2.00 Å(reported)

This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/XrayValidationReportHelpwith speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

MolProbity : 4.02b-467Mogul : 1.8.5 (274361), CSD as541be (2020)

Xtriage (Phenix) : 1.13EDS : 2.11

buster-report : 1.1.7 (2018)Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

Refmac : 5.8.0158CCP4 : 7.0.044 (Gargrove)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : 2.11

https://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#references

Full wwPDB X-ray Structure Validation Report 3HYW

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION

The reported resolution of this entry is 2.00 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

Similar resolution(#Entries, resolution range(Å))

Rfree 130704 8085 (2.00-2.00)Clashscore 141614 9178 (2.00-2.00)

Ramachandran outliers 138981 9054 (2.00-2.00)Sidechain outliers 138945 9053 (2.00-2.00)RSRZ outliers 127900 7900 (2.00-2.00)

The table below summarises the geometric issues observed across the polymeric chains and their�t to the electron density. The red, orange, yellow and green segments on the lower bar indicatethe fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric qualitycriteria respectively. A grey segment represents the fraction of residues that are not modelled.The numeric value for each fraction is indicated below the corresponding segment, with a dotrepresenting fractions


The following table lists non-polymeric compounds, carbohydrate monomers and non-standardresidues in protein, DNA, RNA chains that are outliers for geometric or electron-density-�t crite-ria:

Mol Type Chain Res Chirality Geometry Clashes Electron density3 DCQ A 500 - - X X3 DCQ B 500 - - X X3 DCQ C 500 - - X X3 DCQ D 500 - - X X3 DCQ E 500 - - X X3 DCQ F 500 - - X X4 LMT A 600 - - - X4 LMT B 600 - - - X4 LMT C 600 - - - X4 LMT D 600 - - - X4 LMT E 600 - - - X4 LMT F 600 - - - X6 PS9 A 800 - - X X6 PS9 B 802[A] - - - X6 PS9 B 802[B] - - - X6 PS9 C 800 - - X X6 PS9 D 800 - - X X6 PS9 D 802 - - X X6 PS9 E 800 - - X X6 PS9 F 800 - - X X7 SO4 C 434 - - X -7 SO4 D 431 - - - X7 SO4 F 434 - - X -


2 Entry composition iO

There are 8 unique types of molecules in this entry. The entry contains 22002 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.

Molecule 1 is a protein called Sul�de-quinone reductase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 429Total C N O S3339 2161 553 602 23

0 3 0

1 B 429Total C N O S3340 2161 553 602 24

0 3 0

1 C 429Total C N O S3339 2161 553 602 23

0 3 0

1 D 429Total C N O S3340 2161 553 602 24

0 3 0

1 E 429Total C N O S3339 2161 553 602 23

0 3 0

1 F 429Total C N O S3339 2161 553 602 23

0 3 0

Molecule 2 is FLAVIN-ADENINE DINUCLEOTIDE (three-letter code: FAD) (formula:C27H33N9O15P2).

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#entry_composition


Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1Total C N O P53 27 9 15 2

0 0

2 B 1Total C N O P53 27 9 15 2

0 0

2 C 1Total C N O P53 27 9 15 2

0 0

2 D 1Total C N O P53 27 9 15 2

0 0

2 E 1Total C N O P53 27 9 15 2

0 0

2 F 1Total C N O P53 27 9 15 2

0 0

Molecule 3 is 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione (three-lettercode: DCQ) (formula: C19H30O4).


3 A 1Total C O23 19 4

0 0

3 B 1Total C O23 19 4

0 0

3 C 1Total C O23 19 4

0 0

3 D 1Total C O23 19 4

0 0

3 E 1Total C O23 19 4

0 0

Continued on next page...


Continued from previous page...


3 F 1Total C O23 19 4

0 0

Molecule 4 is DODECYL-BETA-D-MALTOSIDE (three-letter code: LMT) (formula:C24H46O11).


4 A 1Total C O35 24 11

0 0

4 B 1Total C O35 24 11

0 0

4 C 1Total C O35 24 11

0 0

4 D 1Total C O35 24 11

0 0

4 E 1Total C O35 24 11

0 0

4 F 1Total C O35 24 11

0 0

Molecule 5 is HYDROSULFURIC ACID (three-letter code: H2S) (formula: H2S).



5 A 1Total S1 1

0 0

5 B 1Total S1 1

0 0

5 C 1Total S1 1

0 0

5 D 1Total S1 1

0 0

5 E 1Total S1 1

0 0

5 F 1Total S1 1

0 0

Molecule 6 is octathiocane (three-letter code: PS9) (formula: S8).



6 A 1Total S8 8

0 0

6 B 1Total S1 1

0 0

6 B 1Total S3 3

0 1

6 C 1Total S6 6

0 0

6 D 1Total S2 2

0 0

6 D 1Total S1 1

0 0

6 E 1Total S8 8

0 0

6 F 1Total S8 8

0 0

Molecule 7 is SULFATE ION (three-letter code: SO4) (formula: O4S).



7 A 1Total O S5 4 1

0 0

7 A 1Total O S5 4 1

0 0

7 A 1Total O S5 4 1

0 0

7 A 1Total O S5 4 1

0 0

7 A 1Total O S5 4 1

0 0

7 B 1Total O S5 4 1

0 0

7 B 1Total O S5 4 1

0 0

7 B 1Total O S5 4 1

0 0

7 B 1Total O S5 4 1

0 0

7 C 1Total O S5 4 1

0 0

7 C 1Total O S5 4 1

0 0

7 C 1Total O S5 4 1

0 0

7 C 1Total O S5 4 1

0 0

7 D 1Total O S5 4 1

0 0





7 D 1Total O S5 4 1

0 0

7 D 1Total O S5 4 1

0 0

7 D 1Total O S5 4 1

0 0

7 E 1Total O S5 4 1

0 0

7 E 1Total O S5 4 1

0 0

7 E 1Total O S5 4 1

0 0

7 F 1Total O S5 4 1

0 0

7 F 1Total O S5 4 1

0 0

7 F 1Total O S5 4 1

0 0

7 F 1Total O S5 4 1

0 0

Molecule 8 is water.


8 A 214Total O214 214

0 0

8 B 197Total O197 197

0 0

8 C 189Total O189 189

0 0

8 D 160Total O160 160

0 0

8 E 179Total O179 179

0 0

8 F 198Total O198 198

0 0


3 Residue-property plots iO

These plots are drawn for all protein, RNA and DNA chains in the entry. The �rst graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometry and electron density.Residues are color-coded according to the number of geometric quality criteria for which theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor �t to the electron density (RSRZ > 2). Stretches of 2 or moreconsecutive residues without any outlier are shown as a green connector. Residues present in thesample, but not in the model, are shown in grey.

• Molecule 1: Sul�de-quinone reductase

Chain A:

MET

A2•

V5

V6

V7•

I8•

I15•

L24

M25

P26

D27•

L28

L32•

F41•

S92•

Y100

T121

C124

K135

E138•

N142•

P143•

V147

I148

G149

C156

E162

M166

K173•

R177

I185

L191

I199

R204•

N214

D229•

D235

L236•

N237•

H241

E242

V243

P244

A245

T248

M274

V277

N278

F281

Q282

N283

Y286

G293

V294

K312

I317

N327

Y339

I346

C347

I348•

E353•

P366

R367

E368

T372

F381•

K382

L390

V406

L407

L411

K412

V413

K420•

D421

C422

R429

C430•


Chain B:

MET

A2•

V5•

V6

V7•

L24

D27•

L28

D35

F41•

E79

S80

I81

Q91•

Y98

A113

Q116

S120

T121

C124

K135

A141•

I148

G149

C156

P159

L165

R177

F184

I185

V196

I199

N214

I226

I232

L236•

N237•

G238

N239•

E242

M251

V260

A263

A268

V277

F281

Q282

N283

Y286

G293

V294

K303•

K312

I317

N327

Y339

L343•

F351

R367

T372

F381•

K405

V406

L407

E408

I409

K420•

E423•

C430•


Chain C:

MET

A2•

K3

H4

V5

L24

D27•

L28

K29•

P67•

E79•

Q91•

S92•

K95•

I96

I103•

E114•

E118•

C124

E131•

A141•

N142•

G149•

A150•

I151•

P159

F163•

A164•

R177

L191

N214

Y233

E234

D235

H241

K246•

F250•

P270•

M274

V277

N278

R279

C280

F281

Q282

N283

Y286

G293

M316

I317

M320

N327

Y339

A340

P341

R342

L343•

A349

F359

V363•

I364

P365

P366

R367

I371

T372

K373

F381•

L390

R394

V406

C430•


https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#residue_plots


Chain D:

MET

A2•

K3

H4

V5

V6

V7

I8•

Y19

L24

L28

K29•

I30

T31

L32

I33

M50

Q91•

S92•

G93•

K94

K95•

I96

E97•

Y98

L101

V102

I103

A104

T105

G106

P107

G112•

E117•

E118•

T121

C124

K135

A141•

N142•

I148

G149

C156

Y161

E162

L165

M166

L171

G175•

I176

R177

Y178•

F184

I185

S202

V206

N214

P228•

D229•

K230•

L236•

N237•

G238•

N239•

T240•

P257

E258

V259

V260

A268

N269

P270•

A271•

V277

N278

F281

Q282

N283

P284

T285•

Y286

V292

G293

V294

K303•

T304

T308

K312

I317

N327

N334•

N335

P336•

Y339

L343

I346

D350

P366

R367

Y380•

F381

K382

T383

A384

F385

I398

V406

L407

L411

H414

E417

K420•

D421

C422

E423•

C430•


Chain E:

MET

A2•

V5

V6

L24

D27•

L28

I33

F41

T42

A63

P64

I74•

D84•

T87•

Q91•

S92•

G93•

K94•

E97•

Y98

D99

Y100

L101

K108

E114•

E118•

T121

C124

H128

K135

A141•

V147

I148

G149

P159

L165

H168

L171

K172

K173•

R177

F184

I185

L191

R204•

L209

N214

V223

E227•

P228•

L236•

N237•

T240•

A245

F250

P257

E258•

D265•

V277

F281

Q282

N283

Y286

G293

V294

K303•

K312

T313

I317

N327

P336•

Y339

D350

F351

G352

E353•

P366

R367

E368

R369

K382

L390

F402

K405

V406

L407

C430•


Chain F:

MET

A2•

V5

L24

T42

P43

E56•

A63

P64

E72•

Q91•

S92•

E97•

A104

E114•

T121

C124

K134•

K135

L136

Q137

A141•

G149

P159

L165

L171•

R177

I185

V196

I199

N214

Y233

L236

H241

M251

E258•

D265•

V277

N278

R279

C280

F281

Q282

N283

Y286

V292

G293

V294

P300

I301

T304

P305

T308

G309

V310

P311

K312

I317

N327

Y339

I346

C347

D361

P362

V363

R367

E368

R369

T372

K376•

K382

F385

E386

K387

K405

L411

E423•

C430•


4 Data and re�nement statistics iO

Property Value SourceSpace group P 21 21 21 DepositorCell constantsa, b, c, α, β, γ

110.78Å 154.01Å 175.55Å90.00◦ 90.00◦ 90.00◦

Depositor

Resolution (Å)20.45 � 2.0020.45 � 2.00

DepositorEDS

% Data completeness(in resolution range)

96.2 (20.45-2.00)96.2 (20.45-2.00)

DepositorEDS

Rmerge (Not available) DepositorRsym (Not available) Depositor

< I/σ(I) > 1 1.67 (at 2.01Å) XtriageRe�nement program REFMAC 5.2.0019 Depositor

R, Rfree0.200 , 0.2360.227 , 0.257

DepositorDCC

Rfree test set 9757 re�ections (5.02%) wwPDB-VPWilson B-factor (Å2) 33.9 Xtriage

Anisotropy 0.041 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.37 , 43.9 EDS

L-test for twinning2 < |L| > = 0.48, < L2 > = 0.31 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.94 EDSTotal number of atoms 22002 wwPDB-VP

Average B, all atoms (Å2) 36.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Pattersonfunction is 2.40% of the height of the origin peak. No signi�cant pseudotranslation is detected.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric re�ections are 0.5, 0.333 respectively for untwinned datasets,

and 0.375, 0.2 for perfectly twinned datasets.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#data_stats


5 Model quality iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section:LMT, H2S, PS9, SO4, FAD, CSS, DCQ

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol ChainBond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.41 0/3417 0.54 0/46371 B 0.40 0/3417 0.54 0/46371 C 0.40 0/3417 0.54 0/46371 D 0.39 0/3417 0.52 0/46371 E 0.39 0/3417 0.53 0/46371 F 0.39 0/3417 0.53 0/4637All All 0.40 0/20502 0.53 0/27822

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no planarity outliers.

5.2 Too-close contacts iO

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 3339 0 3338 34 01 B 3340 0 3338 33 01 C 3339 0 3338 28 01 D 3340 0 3338 54 01 E 3339 0 3338 43 01 F 3339 0 3338 50 02 A 53 0 29 2 0


https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_qualityhttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#standard_geometryhttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#close_contacts



Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes2 B 53 0 29 0 02 C 53 0 29 0 02 D 53 0 29 6 02 E 53 0 29 0 02 F 53 0 29 7 03 A 23 0 30 16 03 B 23 0 30 23 03 C 23 0 30 32 03 D 23 0 29 34 03 E 23 0 30 18 03 F 23 0 30 19 04 A 35 0 46 2 04 B 35 0 46 6 04 C 35 0 46 5 04 D 35 0 44 1 04 E 35 0 46 4 04 F 35 0 46 6 05 A 1 0 0 1 05 B 1 0 0 1 05 C 1 0 0 1 05 D 1 0 0 1 05 E 1 0 0 1 05 F 1 0 0 1 06 A 8 0 0 2 06 B 4 0 0 1 06 C 6 0 0 2 06 D 3 0 0 3 06 E 8 0 0 2 06 F 8 0 0 2 07 A 25 0 0 0 07 B 20 0 0 0 07 C 20 0 0 5 07 D 20 0 0 0 07 E 15 0 0 1 07 F 20 0 0 4 08 A 214 0 0 1 08 B 197 0 0 0 08 C 189 0 0 2 08 D 160 0 0 1 08 E 179 0 0 1 08 F 198 0 0 2 0All All 22002 0 20655 310 0


The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 7.

All (310) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

3:C:500:DCQ:C15 3:D:500:DCQ:H12 1.19 1.593:C:500:DCQ:H15 3:D:500:DCQ:C12 1.29 1.553:C:500:DCQ:C16 3:D:500:DCQ:H12 1.52 1.373:C:500:DCQ:H15 3:D:500:DCQ:C13 1.52 1.343:C:500:DCQ:H15 3:D:500:DCQ:C14 1.56 1.343:C:500:DCQ:C14 3:D:500:DCQ:H14 1.57 1.323:C:500:DCQ:C15 3:D:500:DCQ:H14A 1.60 1.313:C:500:DCQ:C15 3:D:500:DCQ:C14 2.10 1.273:C:500:DCQ:C14 3:D:500:DCQ:C14 2.12 1.261:A:347[B]:CSS:SG 6:A:800:PS9:S5 2.33 1.253:A:500:DCQ:C13 3:B:500:DCQ:H16A 1.66 1.243:E:500:DCQ:H14A 3:F:500:DCQ:C13 1.71 1.193:C:500:DCQ:C15 3:D:500:DCQ:C12 2.02 1.163:E:500:DCQ:C14 3:F:500:DCQ:H13 1.77 1.153:B:500:DCQ:H15A 4:B:600:LMT:H112 1.11 1.103:E:500:DCQ:H14A 3:F:500:DCQ:H13 1.18 1.093:A:500:DCQ:H16A 3:B:500:DCQ:H13A 1.27 1.083:E:500:DCQ:H12 3:F:500:DCQ:H15 1.18 1.083:B:500:DCQ:C8 3:B:500:DCQ:H1M 1.84 1.08

3:B:500:DCQ:H15A 4:B:600:LMT:C11 1.84 1.061:C:327:ASN:HD21 1:C:339:TYR:H 1.05 1.033:E:500:DCQ:H12 3:F:500:DCQ:C15 1.88 1.033:A:500:DCQ:H13A 3:B:500:DCQ:C16 1.89 1.023:C:500:DCQ:H14A 3:D:500:DCQ:H14 1.02 1.013:E:500:DCQ:C12 3:F:500:DCQ:C15 2.39 1.013:C:500:DCQ:C16 3:D:500:DCQ:C12 2.29 1.003:B:500:DCQ:H8A 3:B:500:DCQ:C1M 1.88 1.003:E:500:DCQ:H12A 3:F:500:DCQ:H15A 1.44 0.981:A:327:ASN:HD21 1:A:339:TYR:H 1.09 0.971:D:8:ILE:HD11 2:D:441:FAD:C2A 1.95 0.973:E:500:DCQ:C12 3:F:500:DCQ:H15 1.95 0.963:A:500:DCQ:H13A 3:B:500:DCQ:H16A 0.97 0.961:E:283:ASN:HD22 1:E:286:TYR:H 1.13 0.953:B:500:DCQ:H8A 3:B:500:DCQ:H1M 0.97 0.953:C:500:DCQ:C13 3:D:500:DCQ:C14 2.45 0.941:E:327:ASN:HD21 1:E:339:TYR:H 1.13 0.941:B:327:ASN:HD21 1:B:339:TYR:H 1.11 0.93





Clashoverlap (Å)

1:D:327:ASN:HD21 1:D:339:TYR:H 1.12 0.923:C:500:DCQ:H16 3:D:500:DCQ:H12 1.51 0.923:C:500:DCQ:C14 3:D:500:DCQ:H14A 1.92 0.911:F:327:ASN:HD21 1:F:339:TYR:H 1.14 0.903:C:500:DCQ:H16B 3:D:500:DCQ:H11A 1.52 0.903:C:500:DCQ:C16 3:D:500:DCQ:H11A 2.02 0.893:E:500:DCQ:C12 3:F:500:DCQ:H15A 2.01 0.893:C:500:DCQ:C13 3:D:500:DCQ:H14A 2.04 0.871:D:283:ASN:HD22 1:D:286:TYR:H 1.22 0.876:D:800:PS9:S3 6:D:802:PS9:S2 2.72 0.87

3:A:500:DCQ:C16 3:B:500:DCQ:H13A 2.03 0.861:B:196:VAL:HG22 1:B:367:ARG:NH1 1.92 0.851:E:293:GLY:HA2 1:E:317:ILE:HD12 1.57 0.856:D:800:PS9:S2 6:D:802:PS9:S2 2.75 0.84

3:B:500:DCQ:C15 4:B:600:LMT:H112 2.04 0.843:C:500:DCQ:C16 3:D:500:DCQ:C11 2.55 0.841:D:367:ARG:H 1:F:214:ASN:HD22 1.26 0.833:A:500:DCQ:C12 3:B:500:DCQ:H16A 2.09 0.834:C:600:LMT:H6'2 7:C:434:SO4:O3 1.79 0.824:C:600:LMT:H5B 7:C:434:SO4:O1 1.80 0.813:E:500:DCQ:C15 3:F:500:DCQ:H13 2.11 0.801:F:283:ASN:HD22 1:F:286:TYR:H 1.27 0.801:A:283:ASN:HD22 1:A:286:TYR:H 1.28 0.791:C:283:ASN:HD22 1:C:286:TYR:H 1.31 0.783:E:500:DCQ:H14A 3:F:500:DCQ:C15 2.12 0.771:A:274:MET:SD 8:A:1113:HOH:O 2.42 0.771:B:196:VAL:HG22 1:B:367:ARG:HH11 1.50 0.773:C:500:DCQ:H13 3:D:500:DCQ:H16B 1.66 0.763:C:500:DCQ:C13 3:D:500:DCQ:H14 2.14 0.761:E:313:THR:O 1:E:317:ILE:HG12 1.85 0.75

1:F:346:ILE:HG22 3:F:500:DCQ:H4MA 1.69 0.743:C:500:DCQ:H14A 3:D:500:DCQ:C14 1.89 0.741:E:283:ASN:ND2 1:E:286:TYR:H 1.87 0.731:B:283:ASN:HD22 1:B:286:TYR:H 1.34 0.721:F:347[A]:CSS:HB2 6:F:800:PS9:S6 2.30 0.723:C:500:DCQ:H16 3:D:500:DCQ:C12 2.14 0.713:C:500:DCQ:H15 3:D:500:DCQ:H14A 1.34 0.711:F:42:THR:HG21 2:F:441:FAD:O4' 1.90 0.711:B:327:ASN:HD21 1:B:339:TYR:N 1.87 0.713:E:500:DCQ:H14A 3:F:500:DCQ:C14 2.21 0.703:C:500:DCQ:H16B 3:D:500:DCQ:C11 2.17 0.69





Clashoverlap (Å)

1:A:124[A]:CYS:SG 5:A:700:H2S:S 2.69 0.691:A:147:VAL:HG13 1:A:248:THR:HG22 1.74 0.691:B:367:ARG:H 1:D:214:ASN:HD22 1.39 0.68

1:E:327:ASN:HD21 1:E:339:TYR:N 1.89 0.681:D:367:ARG:H 1:F:214:ASN:ND2 1.92 0.683:A:500:DCQ:H11 3:B:500:DCQ:C16 2.24 0.671:F:42:THR:HG21 2:F:441:FAD:H3' 1.75 0.673:C:500:DCQ:H13A 3:D:500:DCQ:H14A 1.77 0.673:C:500:DCQ:H15A 3:D:500:DCQ:H14A 1.68 0.671:F:300:PRO:HA 1:F:310:VAL:HG23 1.76 0.661:F:347[B]:CSS:SG 6:F:800:PS9:S6 2.93 0.663:A:500:DCQ:C11 3:B:500:DCQ:C16 2.74 0.651:C:214:ASN:HD22 1:E:367:ARG:H 1.45 0.651:F:137:GLN:NE2 8:F:572:HOH:O 2.29 0.651:E:350:ASP:HB2 1:E:382:LYS:HD3 1.79 0.651:F:385:PHE:CE2 3:F:500:DCQ:H3MB 2.32 0.641:F:293:GLY:HA2 1:F:317:ILE:HG12 1.79 0.641:A:346:ILE:HD11 1:A:411:LEU:CD1 2.28 0.641:C:327:ASN:HD21 1:C:339:TYR:N 1.87 0.641:B:124[A]:CYS:SG 5:B:700:H2S:S 2.74 0.641:D:106:GLY:HA2 1:D:294:VAL:HG13 1.79 0.643:E:500:DCQ:H12A 3:F:500:DCQ:C15 2.15 0.631:D:294:VAL:HA 1:D:312:LYS:HD3 1.80 0.631:C:214:ASN:ND2 1:E:367:ARG:H 1.96 0.634:F:600:LMT:H5B 7:F:434:SO4:S 2.38 0.631:C:124[A]:CYS:SG 5:C:700:H2S:S 2.82 0.633:E:500:DCQ:H15 3:F:500:DCQ:H13 1.79 0.631:E:121:THR:CG2 1:E:135:LYS:HD3 2.29 0.631:B:327:ASN:ND2 1:B:339:TYR:H 1.91 0.621:B:232:ILE:HG12 1:B:242:GLU:HG2 1.81 0.621:B:159:PRO:HB2 1:B:251:MET:HE1 1.81 0.621:F:124[A]:CYS:SG 5:F:700:H2S:S 2.64 0.621:D:162:GLU:HG3 1:D:350:ASP:O 2.00 0.613:A:500:DCQ:H14 3:B:500:DCQ:H14 1.82 0.611:C:327:ASN:ND2 1:C:339:TYR:H 1.88 0.611:F:196:VAL:HG22 1:F:367:ARG:HH11 1.66 0.611:C:235:ASP:OD2 1:C:241:HIS:HE1 1.84 0.604:F:600:LMT:H3B 7:F:434:SO4:O1 2.02 0.601:A:283:ASN:ND2 1:A:286:TYR:H 2.00 0.601:D:414:HIS:HE1 1:D:417:GLU:OE2 1.84 0.601:E:121:THR:HG22 1:E:135:LYS:HD3 1.85 0.59





Clashoverlap (Å)

1:A:367:ARG:H 1:E:214:ASN:HD22 1.48 0.591:F:327:ASN:HD21 1:F:339:TYR:N 1.93 0.591:B:79:GLU:HG3 1:B:91:GLN:HA 1.84 0.591:F:196:VAL:HG22 1:F:367:ARG:NH1 2.18 0.581:E:293:GLY:HA2 1:E:317:ILE:CD1 2.31 0.581:E:327:ASN:ND2 1:E:339:TYR:H 1.94 0.581:F:283:ASN:ND2 1:F:286:TYR:H 2.00 0.581:D:4:HIS:NE2 1:D:31:THR:HG22 2.17 0.58

1:A:214:ASN:HD22 1:C:367:ARG:H 1.50 0.581:A:199:ILE:O 1:A:372:THR:HG21 2.03 0.581:E:6:VAL:HG12 1:E:98:TYR:HB3 1.86 0.571:C:4:HIS:HE1 1:C:96:ILE:HD11 1.69 0.57

4:A:600:LMT:H112 4:B:600:LMT:H101 1.87 0.573:A:500:DCQ:C11 3:B:500:DCQ:H16A 2.34 0.561:B:367:ARG:H 1:D:214:ASN:ND2 2.02 0.563:C:500:DCQ:H16 3:D:500:DCQ:H11A 1.83 0.563:A:500:DCQ:H11 3:B:500:DCQ:H16 1.88 0.561:F:279:ARG:HD3 1:F:430:CYS:HB3 1.87 0.563:A:500:DCQ:C12 3:B:500:DCQ:C16 2.82 0.561:D:149:GLY:HA3 1:D:185:ILE:O 2.06 0.561:A:293:GLY:HA2 1:A:317:ILE:HG12 1.87 0.551:D:8:ILE:HD11 2:D:441:FAD:H2A 1.83 0.553:C:500:DCQ:H13 3:D:500:DCQ:C14 2.34 0.551:F:159:PRO:HB2 1:F:251:MET:HE3 1.88 0.551:D:107:PRO:HD3 1:D:294:VAL:HG11 1.89 0.543:A:500:DCQ:H13 4:A:600:LMT:H111 1.90 0.541:D:346:ILE:HD11 1:D:411:LEU:CD1 2.37 0.541:B:214:ASN:HD22 1:F:367:ARG:H 1.56 0.541:B:199:ILE:O 1:B:372:THR:HG21 2.07 0.54

1:D:304:THR:OG1 1:D:308:THR:HB 2.08 0.541:F:104:ALA:HB2 1:F:292:VAL:CG1 2.38 0.544:F:600:LMT:H5B 7:F:434:SO4:O1 2.08 0.541:B:156[A]:CSS:SG 6:B:800:PS9:S2 3.05 0.533:C:500:DCQ:H13 3:D:500:DCQ:C16 2.38 0.531:D:293:GLY:HA2 1:D:317:ILE:HG12 1.90 0.531:E:405:LYS:HD3 1:F:387:LYS:HD2 1.90 0.533:E:500:DCQ:C14 3:F:500:DCQ:C15 2.85 0.531:C:279:ARG:HD3 1:C:430:CYS:HB3 1.90 0.534:C:600:LMT:C6B 7:C:434:SO4:O3 2.53 0.531:F:304:THR:OG1 1:F:308:THR:HB 2.07 0.531:F:42:THR:CG2 1:F:43:PRO:HD3 2.38 0.53





Clashoverlap (Å)

1:D:177:ARG:NH2 8:D:1251:HOH:O 2.43 0.521:E:5:VAL:HG22 1:E:100:TYR:HB2 1.90 0.521:F:42:THR:HG23 1:F:43:PRO:HD3 1.92 0.521:B:293:GLY:HA2 1:B:317:ILE:HG12 1.92 0.521:A:367:ARG:H 1:E:214:ASN:ND2 2.07 0.511:D:104:ALA:HB2 1:D:292:VAL:CG2 2.39 0.511:D:283:ASN:ND2 1:D:286:TYR:H 2.01 0.511:E:41:PHE:HB2 1:E:390:LEU:HD11 1.92 0.511:E:159:PRO:HD3 6:E:800:PS9:S3 2.51 0.511:E:6:VAL:HG12 1:E:98:TYR:CB 2.41 0.511:B:277:VAL:HB 1:B:281:PHE:HA 1.92 0.511:F:346:ILE:HD11 1:F:411:LEU:CD1 2.41 0.511:C:274:MET:HE1 8:C:501:HOH:O 2.10 0.501:C:283:ASN:ND2 1:C:286:TYR:H 2.04 0.501:F:382:LYS:NZ 2:F:441:FAD:O4 2.44 0.501:D:8:ILE:HD12 1:D:33:ILE:O 2.11 0.501:D:50:MET:HG3 1:D:166:MET:HE2 1.94 0.501:B:121:THR:CG2 1:B:135:LYS:HD3 2.42 0.501:B:149:GLY:HA3 1:B:185:ILE:O 2.12 0.503:C:500:DCQ:H16 3:D:500:DCQ:C11 2.32 0.501:C:214:ASN:HD21 1:E:366:PRO:HA 1.76 0.493:A:500:DCQ:H11 3:B:500:DCQ:H16A 1.94 0.491:F:121:THR:CG2 1:F:135:LYS:HD3 2.42 0.491:F:327:ASN:ND2 1:F:339:TYR:H 1.96 0.491:B:6:VAL:HG13 1:B:98:TYR:HB3 1.94 0.491:E:149:GLY:HA3 1:E:185:ILE:O 2.12 0.491:A:156[A]:CSS:SG 6:A:800:PS9:S2 3.10 0.491:F:405:LYS:HE2 8:F:481:HOH:O 2.13 0.491:B:283:ASN:ND2 1:B:286:TYR:H 2.09 0.491:F:104:ALA:HB2 1:F:292:VAL:HG13 1.95 0.481:D:366:PRO:HA 1:F:214:ASN:HD21 1.78 0.481:D:385:PHE:CE2 3:D:500:DCQ:H3MB 2.48 0.481:F:149:GLY:HA3 1:F:185:ILE:O 2.14 0.481:A:406:VAL:HG21 3:A:500:DCQ:H14A 1.95 0.481:B:294:VAL:HA 1:B:312:LYS:HD3 1.96 0.481:D:327:ASN:ND2 1:D:339:TYR:H 1.94 0.471:D:327:ASN:HD21 1:D:339:TYR:N 1.95 0.471:C:394:ARG:NH2 8:C:858:HOH:O 2.47 0.474:E:600:LMT:C6B 4:F:600:LMT:H1' 2.45 0.471:F:277:VAL:HB 1:F:281:PHE:HA 1.96 0.471:A:407:LEU:HB3 1:A:413:VAL:HG13 1.97 0.47





Clashoverlap (Å)

1:D:202:SER:O 1:D:206:VAL:HG23 2.15 0.471:C:293:GLY:HA2 1:C:317:ILE:HG12 1.96 0.461:E:128:HIS:HE1 8:E:469:HOH:O 1.96 0.461:C:277:VAL:HB 1:C:281:PHE:HA 1.97 0.461:E:147:VAL:CG1 1:E:245:ALA:HB2 2.46 0.461:D:260:VAL:HG12 1:D:268:ALA:HB2 1.96 0.461:E:124[A]:CYS:SG 5:E:700:H2S:S 3.04 0.463:B:500:DCQ:C15 4:B:600:LMT:C11 2.75 0.461:D:8:ILE:HG22 1:D:103:ILE:HA 1.98 0.461:D:6:VAL:HG13 1:D:101:LEU:HD12 1.98 0.461:E:406:VAL:HG11 3:E:500:DCQ:H13A 1.97 0.461:F:385:PHE:HE2 3:F:500:DCQ:H3MB 1.79 0.462:A:441:FAD:H9 2:A:441:FAD:H1'1 1.80 0.451:F:42:THR:CG2 2:F:441:FAD:H3' 2.45 0.451:D:6:VAL:HG13 1:D:101:LEU:CD1 2.46 0.451:A:121:THR:CG2 1:A:135:LYS:HD3 2.46 0.451:A:366:PRO:O 1:A:429:ARG:NH1 2.50 0.451:B:381:PHE:HE1 4:B:600:LMT:H61 1.82 0.451:C:394:ARG:NH1 7:C:432:SO4:O1 2.49 0.453:A:500:DCQ:H1M 3:A:500:DCQ:H7 1.76 0.451:D:148:ILE:O 1:D:184:PHE:HA 2.17 0.45

1:F:196:VAL:HG21 1:F:363:VAL:HG13 1.99 0.451:A:149:GLY:HA3 1:A:185:ILE:O 2.17 0.441:D:19:TYR:CD2 1:D:398:ILE:HG12 2.53 0.441:C:316:MET:O 1:C:320:MET:HG3 2.17 0.44

1:A:214:ASN:HD21 1:C:365:PRO:HB3 1.82 0.441:A:382:LYS:NZ 2:A:441:FAD:O4 2.49 0.44

1:B:165:LEU:HD13 1:B:351:PHE:CD1 2.52 0.441:C:406:VAL:HG22 1:D:384:ALA:HB1 1.99 0.441:F:233:TYR:CZ 1:F:241:HIS:HB2 2.52 0.441:D:161:TYR:CE1 1:D:206:VAL:HG11 2.52 0.441:F:294:VAL:HA 1:F:312:LYS:HD3 1.98 0.441:B:381:PHE:HE2 3:B:500:DCQ:H1MB 1.83 0.441:D:346:ILE:O 3:D:500:DCQ:H4MB 2.18 0.441:D:8:ILE:CD1 2:D:441:FAD:C2A 2.84 0.441:A:277:VAL:HB 1:A:281:PHE:HA 1.98 0.443:C:500:DCQ:H7 3:C:500:DCQ:H1M 1.79 0.441:E:6:VAL:HG13 1:E:101:LEU:CD1 2.47 0.444:E:600:LMT:H3B 7:E:434:SO4:O2 2.17 0.441:F:199:ILE:O 1:F:372:THR:HG21 2.17 0.441:B:148:ILE:O 1:B:184:PHE:HA 2.18 0.44





Clashoverlap (Å)

1:B:113:ALA:HB3 1:B:116:GLN:HB2 1.99 0.444:C:600:LMT:H1' 4:D:600:LMT:O2B 2.16 0.442:F:441:FAD:H9 2:F:441:FAD:H1'1 1.79 0.44

1:B:407:LEU:HD21 3:B:500:DCQ:H8 1.98 0.431:D:8:ILE:HD11 2:D:441:FAD:N1A 2.28 0.43

1:E:209:LEU:HD21 1:E:351:PHE:CE2 2.53 0.433:B:500:DCQ:O2 3:B:500:DCQ:H3MB 2.18 0.431:D:6:VAL:HG12 1:D:98:TYR:HB3 1.99 0.431:E:108:LYS:HD2 1:E:257:PRO:HA 1.99 0.431:E:294:VAL:HA 1:E:312:LYS:HD3 2.00 0.431:A:214:ASN:ND2 1:C:366:PRO:HA 2.33 0.431:D:6:VAL:HG12 1:D:98:TYR:CB 2.48 0.431:F:236:LEU:HD11 1:F:305:PRO:HB3 2.00 0.431:B:120:SER:HB2 1:B:226:ILE:HG21 2.01 0.431:D:8:ILE:CG2 1:D:103:ILE:HA 2.48 0.431:D:19:TYR:HD2 1:D:398:ILE:HG12 1.84 0.431:E:402:PHE:HE2 3:E:500:DCQ:H13 1.84 0.431:A:346:ILE:HD11 1:A:411:LEU:HD12 1.98 0.431:A:278:ASN:HB2 1:A:422:CYS:O 2.19 0.431:D:277:VAL:HB 1:D:281:PHE:HA 2.01 0.434:E:600:LMT:H6'2 4:F:600:LMT:H1' 2.00 0.431:A:235:ASP:OD2 1:A:241:HIS:HE1 2.00 0.431:A:368:GLU:O 1:E:172:LYS:HE3 2.19 0.43

1:D:124[A]:CYS:SG 5:D:700:H2S:S 3.07 0.431:A:147:VAL:HG12 1:A:245:ALA:HB2 2.00 0.421:D:382:LYS:NZ 2:D:441:FAD:O4 2.47 0.421:F:42:THR:HG21 2:F:441:FAD:C4' 2.48 0.421:D:121:THR:CG2 1:D:135:LYS:HD3 2.48 0.421:F:196:VAL:HG23 1:F:301:ILE:CD1 2.49 0.423:E:500:DCQ:C14 3:F:500:DCQ:H15 2.48 0.421:B:81:ILE:HG23 1:B:263:ALA:HB2 2.00 0.421:D:278:ASN:HB2 1:D:422:CYS:O 2.19 0.421:E:168:HIS:ND1 1:E:177:ARG:HD3 2.35 0.421:B:405:LYS:O 1:B:409:ILE:HG23 2.19 0.421:E:148:ILE:O 1:E:184:PHE:HA 2.19 0.42

1:D:156[A]:CSS:SG 6:D:800:PS9:S2 3.17 0.421:F:42:THR:HG21 2:F:441:FAD:C3' 2.44 0.424:E:600:LMT:O5B 4:F:600:LMT:H3' 2.19 0.421:C:349:ALA:HB2 6:C:800:PS9:S6 2.59 0.421:E:283:ASN:HD22 1:E:286:TYR:N 1.97 0.421:E:6:VAL:HG13 1:E:101:LEU:HD13 2.01 0.42





Clashoverlap (Å)

1:F:369:ARG:NH1 7:F:431:SO4:O3 2.52 0.421:A:25:MET:SD 1:A:28:LEU:HG 2.60 0.421:C:373:LYS:NZ 4:C:600:LMT:H11 2.35 0.421:D:257:PRO:HB2 1:D:259:VAL:HG12 2.02 0.411:C:233:TYR:CZ 1:C:241:HIS:HB2 2.56 0.411:D:257:PRO:HG2 1:D:260:VAL:HG23 2.01 0.411:B:214:ASN:ND2 1:F:367:ARG:H 2.16 0.411:E:277:VAL:HB 1:E:281:PHE:HA 2.03 0.411:B:260:VAL:HG12 1:B:268:ALA:HB2 2.01 0.411:E:223:VAL:HG21 1:E:250:PHE:CE1 2.55 0.411:A:327:ASN:HD21 1:A:339:TYR:N 1.94 0.411:A:162:GLU:O 1:A:166:MET:HG3 2.20 0.41

1:C:159:PRO:HD3 6:C:800:PS9:S2 2.61 0.411:D:406:VAL:HG21 3:D:500:DCQ:H15A 2.02 0.411:E:159:PRO:HD3 6:E:800:PS9:S4 2.61 0.411:D:366:PRO:HA 1:F:214:ASN:ND2 2.35 0.411:D:294:VAL:HG12 2:D:441:FAD:O2P 2.21 0.411:F:361:ASP:HA 1:F:362:PRO:HA 1.93 0.411:E:63:ALA:HB3 1:E:64:PRO:HD3 2.03 0.411:E:33:ILE:HG12 1:E:74:ILE:CG2 2.51 0.411:F:63:ALA:HB3 1:F:64:PRO:HD3 2.03 0.401:A:147:VAL:CG1 1:A:245:ALA:HB2 2.52 0.407:C:431:SO4:O4 1:E:369:ARG:NH1 2.55 0.401:A:5:VAL:HG22 1:A:100:TYR:HB2 2.04 0.401:C:359:PHE:HB3 1:C:371:ILE:HB 2.04 0.401:A:294:VAL:HA 1:A:312:LYS:HD3 2.04 0.401:C:341:PRO:HB2 1:C:343:LEU:HD13 2.02 0.40

There are no symmetry-related clashes.

5.3 Torsion angles iO

5.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all X-ray entries followed by that with respect to entriesof similar resolution.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#torsion_angleshttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#protein_backbone


Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 426/430 (99%) 419 (98%) 7 (2%) 0 100 100

1 B 426/430 (99%) 417 (98%) 9 (2%) 0 100 100

1 C 426/430 (99%) 419 (98%) 7 (2%) 0 100 100

1 D 426/430 (99%) 421 (99%) 5 (1%) 0 100 100

1 E 426/430 (99%) 417 (98%) 9 (2%) 0 100 100

1 F 426/430 (99%) 419 (98%) 7 (2%) 0 100 100

All All 2556/2580 (99%) 2512 (98%) 44 (2%) 0 100 100

There are no Ramachandran outliers to report.

5.3.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similarresolution.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 355/355 (100%) 347 (98%) 8 (2%) 50 53

1 B 355/355 (100%) 345 (97%) 10 (3%) 43 44

1 C 355/355 (100%) 347 (98%) 8 (2%) 50 53

1 D 355/355 (100%) 346 (98%) 9 (2%) 47 49

1 E 355/355 (100%) 345 (97%) 10 (3%) 43 44

1 F 355/355 (100%) 349 (98%) 6 (2%) 60 65

All All 2130/2130 (100%) 2079 (98%) 51 (2%) 49 51

All (51) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 24 LEU1 A 28 LEU1 A 177 ARG1 A 191 LEU1 A 243 VAL1 A 390 LEU1 A 407 LEU


https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#protein_sidechains



Mol Chain Res Type1 A 413 VAL1 B 5 VAL1 B 6 VAL1 B 24 LEU1 B 28 LEU1 B 35 ASP1 B 81 ILE1 B 177 ARG1 B 343 LEU1 B 407 LEU1 B 409 ILE1 C 5 VAL1 C 24 LEU1 C 96 ILE1 C 142 ASN1 C 177 ARG1 C 191 LEU1 C 343 LEU1 C 390 LEU1 D 24 LEU1 D 28 LEU1 D 165 LEU1 D 171 LEU1 D 177 ARG1 D 294 VAL1 D 308 THR1 D 343 LEU1 D 407 LEU1 E 24 LEU1 E 28 LEU1 E 42 THR1 E 147 VAL1 E 165 LEU1 E 171 LEU1 E 177 ARG1 E 191 LEU1 E 390 LEU1 E 407 LEU1 F 5 VAL1 F 24 LEU1 F 165 LEU1 F 177 ARG




Mol Chain Res Type1 F 236 LEU1 F 308 THR

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (55) suchsidechains are listed below:

Mol Chain Res Type1 A 70 ASN1 A 214 ASN1 A 237 ASN1 A 241 HIS1 A 283 ASN1 A 327 ASN1 A 379 HIS1 A 395 ASN1 B 23 ASN1 B 119 ASN1 B 128 HIS1 B 214 ASN1 B 241 HIS1 B 283 ASN1 B 327 ASN1 B 334 ASN1 B 379 HIS1 B 395 ASN1 C 23 ASN1 C 128 HIS1 C 214 ASN1 C 237 ASN1 C 241 HIS1 C 283 ASN1 C 327 ASN1 C 379 HIS1 C 395 ASN1 D 128 HIS1 D 214 ASN1 D 237 ASN1 D 241 HIS1 D 283 ASN1 D 326 HIS1 D 327 ASN1 D 379 HIS1 D 395 ASN




Mol Chain Res Type1 D 414 HIS1 E 23 ASN1 E 128 HIS1 E 133 GLN1 E 137 GLN1 E 214 ASN1 E 237 ASN1 E 241 HIS1 E 283 ASN1 E 327 ASN1 E 379 HIS1 E 395 ASN1 F 23 ASN1 F 128 HIS1 F 214 ASN1 F 283 ASN1 F 327 ASN1 F 379 HIS1 F 395 ASN

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

24 non-standard protein/DNA/RNA residues are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 21 CSS B 347[B] 6 4,6,7 1.09 0 1,6,8 1.36 01 CSS B 347[A] - 4,5,7 1.15 0 1,5,8 0.85 01 CSS F 156[B] 6 4,6,7 0.96 0 1,6,8 0.05 01 CSS F 156[A] - 4,5,7 0.98 0 1,5,8 1.07 0

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#rnahttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#nonstandard_residues_and_ligands



Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 21 CSS D 156[A] - 4,5,7 1.03 0 1,5,8 1.11 01 CSS A 347[A] - 4,5,7 1.46 1 (25%) 1,5,8 2.42 1 (100%)

1 CSS A 347[B] - 4,5,7 1.40 1 (25%) 1,5,8 2.65 1 (100%)1 CSS D 156[B] 6 4,6,7 1.05 0 1,6,8 0.11 01 CSS C 156[B] 6 4,6,7 1.03 0 1,6,8 0.08 01 CSS C 156[A] - 4,5,7 1.00 0 1,5,8 0.85 01 CSS A 156[A] - 4,5,7 1.07 0 1,5,8 0.40 01 CSS A 156[B] 6 4,6,7 1.08 0 1,6,8 0.41 01 CSS F 347[B] - 4,5,7 1.33 0 1,5,8 1.76 01 CSS F 347[A] - 4,5,7 1.54 1 (25%) 1,5,8 1.87 01 CSS B 156[B] 6 4,6,7 1.06 0 1,6,8 0.33 01 CSS B 156[A] - 4,5,7 1.02 0 1,5,8 0.96 01 CSS E 347[A] - 4,5,7 1.38 1 (25%) 1,5,8 1.90 0

1 CSS E 347[B] - 4,5,7 1.35 1 (25%) 1,5,8 2.20 1 (100%)1 CSS E 156[A] - 4,5,7 1.06 0 1,5,8 0.58 01 CSS D 347[A] - 4,5,7 1.04 0 1,5,8 1.12 01 CSS E 156[B] 6 4,6,7 1.02 0 1,6,8 0.54 01 CSS C 347[B] - 4,5,7 1.33 0 1,5,8 2.16 1 (100%)1 CSS D 347[B] 6 4,6,7 0.99 0 1,6,8 1.23 01 CSS C 347[A] - 4,5,7 1.48 1 (25%) 1,5,8 2.22 1 (100%)

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

Mol Type Chain Res Link Chirals Torsions Rings1 CSS B 347[B] 6 - 1/1/5/7 -1 CSS B 347[A] - - 0/1/4/7 -1 CSS F 156[B] 6 - 0/1/5/7 -1 CSS F 156[A] - - 1/1/4/7 -1 CSS D 156[A] - - 1/1/4/7 -1 CSS A 347[A] - - 0/1/4/7 -1 CSS A 347[B] - - 1/1/4/7 -1 CSS D 156[B] 6 - 0/1/5/7 -1 CSS C 156[B] 6 - 0/1/5/7 -1 CSS C 156[A] - - 1/1/4/7 -1 CSS A 156[A] - - 1/1/4/7 -1 CSS A 156[B] 6 - 0/1/5/7 -1 CSS F 347[B] - - 1/1/4/7 -1 CSS F 347[A] - - 0/1/4/7 -




Mol Type Chain Res Link Chirals Torsions Rings1 CSS B 156[B] 6 - 0/1/5/7 -1 CSS B 156[A] - - 1/1/4/7 -1 CSS E 347[A] - - 0/1/4/7 -1 CSS E 347[B] - - 1/1/4/7 -1 CSS E 156[A] - - 1/1/4/7 -1 CSS D 347[A] - - 0/1/4/7 -1 CSS E 156[B] 6 - 0/1/5/7 -1 CSS C 347[B] - - 1/1/4/7 -1 CSS D 347[B] 6 - 1/1/5/7 -1 CSS C 347[A] - - 0/1/4/7 -

All (6) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)1 F 347[A] CSS CB-SG -2.50 1.76 1.811 A 347[A] CSS CB-SG -2.35 1.76 1.811 C 347[A] CSS CB-SG -2.31 1.76 1.811 A 347[B] CSS CB-SG -2.18 1.76 1.811 E 347[A] CSS CB-SG -2.15 1.77 1.811 E 347[B] CSS CB-SG -2.06 1.77 1.81

All (5) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 347[B] CSS CA-CB-SG -2.65 108.74 114.441 A 347[A] CSS CA-CB-SG -2.42 109.22 114.441 C 347[A] CSS CA-CB-SG -2.22 109.65 114.441 E 347[B] CSS CA-CB-SG -2.20 109.69 114.441 C 347[B] CSS CA-CB-SG -2.16 109.78 114.44


All (12) torsion outliers are listed below:

Mol Chain Res Type Atoms1 B 347[B] CSS N-CA-CB-SG1 A 347[B] CSS N-CA-CB-SG1 F 347[B] CSS N-CA-CB-SG1 E 347[B] CSS N-CA-CB-SG1 C 347[B] CSS N-CA-CB-SG1 D 347[B] CSS N-CA-CB-SG1 F 156[A] CSS N-CA-CB-SG




Mol Chain Res Type Atoms1 D 156[A] CSS N-CA-CB-SG1 C 156[A] CSS N-CA-CB-SG1 A 156[A] CSS N-CA-CB-SG1 B 156[A] CSS N-CA-CB-SG1 E 156[A] CSS N-CA-CB-SG

There are no ring outliers.

6 monomers are involved in 6 short contacts:

Mol Chain Res Type Clashes Symm-Clashes1 D 156[A] CSS 1 01 A 347[B] CSS 1 01 A 156[A] CSS 1 01 F 347[B] CSS 1 01 F 347[A] CSS 1 01 B 156[A] CSS 1 0

5.5 Carbohydrates iO

There are no carbohydrates in this entry.

5.6 Ligand geometry iO

Of 57 ligands modelled in this entry, 8 are modelled with single atom - leaving 49 for Mogulanalysis.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).


Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 23 DCQ C 500 - 23,23,23 2.25 7 (30%) 26,29,29 0.96 1 (3%)

3 DCQ D 500 - 23,23,23 2.25 7 (30%) 26,29,29 1.01 1 (3%)

3 DCQ F 500 - 23,23,23 2.37 8 (34%) 26,29,29 1.04 2 (7%)

2 FAD F 441 5 51,58,58 1.08 3 (5%) 60,89,89 1.62 8 (13%)

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#nonstandard_residues_and_ligands



Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 24 LMT A 600 - 36,36,36 0.49 0 47,47,47 0.69 1 (2%)7 SO4 F 434 - 4,4,4 0.14 0 6,6,6 0.13 07 SO4 A 431 - 4,4,4 0.15 0 6,6,6 0.06 07 SO4 B 432 - 4,4,4 0.15 0 6,6,6 0.19 06 PS9 F 800 1 8,8,8 0.87 0 8,8,8 1.27 06 PS9 A 800 1 8,8,8 0.90 0 8,8,8 1.14 04 LMT B 600 - 36,36,36 0.51 0 47,47,47 0.76 1 (2%)7 SO4 A 434 - 4,4,4 0.13 0 6,6,6 0.06 07 SO4 B 431 - 4,4,4 0.15 0 6,6,6 0.07 04 LMT F 600 - 36,36,36 0.54 0 47,47,47 0.83 1 (2%)7 SO4 C 431 - 4,4,4 0.15 0 6,6,6 0.06 06 PS9 B 802[B] - 0,1,8 0.00 - -2 FAD D 441 5 51,58,58 1.09 2 (3%) 60,89,89 1.63 8 (13%)6 PS9 B 802[A] - 0,1,8 0.00 - -7 SO4 D 433 - 4,4,4 0.15 0 6,6,6 0.06 07 SO4 B 433 - 4,4,4 0.15 0 6,6,6 0.05 07 SO4 D 434 - 4,4,4 0.16 0 6,6,6 0.12 07 SO4 E 434 - 4,4,4 0.14 0 6,6,6 0.11 07 SO4 C 434 - 4,4,4 0.15 0 6,6,6 0.07 02 FAD A 441 5 51,58,58 1.11 2 (3%) 60,89,89 1.56 7 (11%)

2 FAD C 441 5 51,58,58 1.03 1 (1%) 60,89,89 1.68 8 (13%)

3 DCQ E 500 - 23,23,23 2.24 7 (30%) 26,29,29 0.99 07 SO4 A 432 - 4,4,4 0.17 0 6,6,6 0.12 07 SO4 C 432 - 4,4,4 0.17 0 6,6,6 0.12 07 SO4 F 432 - 4,4,4 0.17 0 6,6,6 0.08 07 SO4 F 431 - 4,4,4 0.15 0 6,6,6 0.14 07 SO4 D 431 - 4,4,4 0.15 0 6,6,6 0.08 06 PS9 E 800 1 8,8,8 0.92 0 8,8,8 0.96 04 LMT D 600 - 36,36,36 0.49 0 47,47,47 0.88 2 (4%)7 SO4 D 432 - 4,4,4 0.14 0 6,6,6 0.15 03 DCQ B 500 - 23,23,23 2.31 7 (30%) 26,29,29 0.75 0

4 LMT C 600 - 36,36,36 0.55 1 (2%) 47,47,47 0.73 1 (2%)7 SO4 C 433 - 4,4,4 0.11 0 6,6,6 0.28 02 FAD B 441 5 51,58,58 1.06 2 (3%) 60,89,89 1.52 7 (11%)

4 LMT E 600 - 36,36,36 0.51 0 47,47,47 0.91 2 (4%)7 SO4 B 434 - 4,4,4 0.14 0 6,6,6 0.15 06 PS9 C 800 1 3,5,8 1.61 0 2,4,8 0.85 07 SO4 A 433 - 4,4,4 0.14 0 6,6,6 0.21 06 PS9 D 800 1 0,1,8 0.00 - -7 SO4 E 433 - 4,4,4 0.12 0 6,6,6 0.20 0



Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 22 FAD E 441 5 51,58,58 1.10 2 (3%) 60,89,89 1.61 7 (11%)7 SO4 F 433 - 4,4,4 0.13 0 6,6,6 0.26 07 SO4 E 432 - 4,4,4 0.15 0 6,6,6 0.10 03 DCQ A 500 - 23,23,23 2.24 7 (30%) 26,29,29 0.94 1 (3%)7 SO4 A 435 - 4,4,4 0.15 0 6,6,6 0.06 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

Mol Type Chain Res Link Chirals Torsions Rings3 DCQ C 500 - - 7/14/38/38 0/1/1/1

3 DCQ D 500 - - 6/14/38/38 0/1/1/1

3 DCQ F 500 - - 7/14/38/38 0/1/1/1

2 FAD F 441 5 - 4/30/50/50 0/6/6/6

4 LMT A 600 - - 8/21/61/61 0/2/2/26 PS9 F 800 1 - - 0/1/1/16 PS9 A 800 1 - - 0/1/1/14 LMT B 600 - - 10/21/61/61 0/2/2/2

2 FAD D 441 5 - 5/30/50/50 0/6/6/62 FAD A 441 5 - 1/30/50/50 0/6/6/62 FAD C 441 5 - 3/30/50/50 0/6/6/6

3 DCQ E 500 - - 3/14/38/38 0/1/1/16 PS9 E 800 1 - - 0/1/1/14 LMT D 600 - - 10/21/61/61 0/2/2/2

3 DCQ B 500 - - 11/14/38/38 0/1/1/1

4 LMT C 600 - - 13/21/61/61 0/2/2/22 FAD B 441 5 - 1/30/50/50 0/6/6/64 LMT E 600 - - 18/21/61/61 0/2/2/26 PS9 C 800 1 - 1/3/3/8 -2 FAD E 441 5 - 3/30/50/50 0/6/6/6

4 LMT F 600 - - 11/21/61/61 0/2/2/2

3 DCQ A 500 - - 5/14/38/38 0/1/1/1

All (56) bond length outliers are listed below:


Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 B 500 DCQ O5-C5 6.32 1.37 1.233 F 500 DCQ O5-C5 6.21 1.36 1.233 D 500 DCQ O5-C5 6.21 1.36 1.233 C 500 DCQ O5-C5 6.20 1.36 1.233 B 500 DCQ O2-C2 6.15 1.36 1.233 A 500 DCQ O5-C5 6.14 1.36 1.233 E 500 DCQ O2-C2 6.04 1.36 1.233 E 500 DCQ O5-C5 6.04 1.36 1.233 C 500 DCQ O2-C2 6.03 1.36 1.233 A 500 DCQ O2-C2 6.01 1.36 1.233 F 500 DCQ O2-C2 5.99 1.36 1.233 D 500 DCQ O2-C2 5.98 1.36 1.232 A 441 FAD O4-C4 4.96 1.37 1.242 E 441 FAD O4-C4 4.66 1.36 1.242 F 441 FAD O4-C4 4.63 1.36 1.242 B 441 FAD O4-C4 4.56 1.36 1.242 D 441 FAD O4-C4 4.48 1.35 1.242 C 441 FAD O4-C4 4.36 1.35 1.243 B 500 DCQ C3-C2 -3.38 1.39 1.483 C 500 DCQ C3-C2 -3.34 1.39 1.483 D 500 DCQ C3-C2 -3.34 1.39 1.483 F 500 DCQ C3-C2 -3.30 1.39 1.483 E 500 DCQ C3-C2 -3.29 1.39 1.483 F 500 DCQ C4-C5 -3.27 1.39 1.483 B 500 DCQ C4-C5 -3.27 1.39 1.483 A 500 DCQ C3-C2 -3.27 1.39 1.483 A 500 DCQ C4-C5 -3.23 1.39 1.483 E 500 DCQ C4-C5 -3.22 1.39 1.483 C 500 DCQ C4-C5 -3.17 1.39 1.483 D 500 DCQ C4-C5 -3.10 1.40 1.483 B 500 DCQ C6-C1 3.01 1.40 1.353 F 500 DCQ C6-C1 2.80 1.40 1.353 F 500 DCQ C16-C15 2.74 1.72 1.493 E 500 DCQ C6-C1 2.74 1.40 1.353 D 500 DCQ C6-C1 2.74 1.40 1.352 E 441 FAD C10-N1 2.67 1.36 1.333 C 500 DCQ C6-C1 2.63 1.40 1.353 A 500 DCQ C6-C1 2.62 1.40 1.352 A 441 FAD C10-N1 2.54 1.36 1.333 A 500 DCQ C6-C5 -2.51 1.39 1.463 E 500 DCQ C6-C5 -2.47 1.39 1.463 F 500 DCQ C6-C5 -2.46 1.39 1.463 D 500 DCQ C6-C5 -2.39 1.39 1.46




Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 D 441 FAD C10-N1 2.37 1.36 1.333 C 500 DCQ C6-C5 -2.37 1.40 1.463 B 500 DCQ C6-C5 -2.34 1.40 1.463 B 500 DCQ C1-C2 -2.28 1.39 1.472 B 441 FAD C10-N1 2.14 1.36 1.333 C 500 DCQ C1-C2 -2.13 1.39 1.473 F 500 DCQ C1-C2 -2.12 1.39 1.474 C 600 LMT O1'-C1' 2.11 1.43 1.402 F 441 FAD C10-N1 2.11 1.36 1.333 E 500 DCQ C1-C2 -2.11 1.39 1.473 A 500 DCQ C1-C2 -2.10 1.39 1.473 D 500 DCQ C1-C2 -2.10 1.39 1.472 F 441 FAD C4X-N5 2.08 1.36 1.33

All (58) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 D 441 FAD C4-N3-C2 6.44 120.58 115.142 E 441 FAD C4-N3-C2 6.22 120.39 115.142 C 441 FAD C4-N3-C2 6.16 120.34 115.142 A 441 FAD C4-N3-C2 5.78 120.02 115.142 F 441 FAD C4-N3-C2 5.62 119.89 115.142 C 441 FAD N3A-C2A-N1A -5.36 120.31 128.682 E 441 FAD N3A-C2A-N1A -5.22 120.51 128.682 B 441 FAD C4-N3-C2 5.22 119.55 115.142 A 441 FAD N3A-C2A-N1A -5.09 120.72 128.682 F 441 FAD N3A-C2A-N1A -5.06 120.78 128.682 B 441 FAD N3A-C2A-N1A -4.97 120.91 128.682 C 441 FAD C1'-N10-C9A 4.86 122.11 118.292 D 441 FAD N3A-C2A-N1A -4.80 121.18 128.682 D 441 FAD C1'-N10-C9A 4.30 121.68 118.292 F 441 FAD C5X-C9A-N10 4.07 120.66 117.722 B 441 FAD C5X-C9A-N10 3.90 120.54 117.722 A 441 FAD C5X-C9A-N10 3.71 120.41 117.722 E 441 FAD C5X-C9A-N10 3.67 120.37 117.722 D 441 FAD C5X-C9A-N10 3.65 120.36 117.722 E 441 FAD C1'-N10-C9A 3.61 121.13 118.292 A 441 FAD C4X-N5-C5X 3.56 120.33 116.772 B 441 FAD C1'-N10-C9A 3.42 120.98 118.292 C 441 FAD C5X-C9A-N10 3.36 120.15 117.722 E 441 FAD C4X-N5-C5X 3.08 119.85 116.774 C 600 LMT O1B-C4'-C3' 2.95 115.13 107.28




Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 F 441 FAD C4X-N5-C5X 2.95 119.72 116.772 A 441 FAD C4X-C4-N3 -2.82 119.58 123.432 F 441 FAD C1'-N10-C9A 2.75 120.45 118.294 E 600 LMT O1B-C4'-C3' 2.62 114.25 107.284 F 600 LMT O1B-C1B-C2B 2.59 114.82 108.102 B 441 FAD C4X-N5-C5X 2.57 119.34 116.772 C 441 FAD C4X-N5-C5X 2.49 119.26 116.774 D 600 LMT C1B-O5B-C5B 2.49 118.57 113.692 C 441 FAD C4X-C4-N3 -2.48 120.03 123.434 E 600 LMT O1B-C4'-C5' 2.47 116.21 109.452 D 441 FAD C4X-N5-C5X 2.43 119.20 116.772 E 441 FAD C4X-C4-N3 -2.39 120.16 123.432 B 441 FAD C9A-N10-C10 -2.37 118.80 121.913 F 500 DCQ C3M-O3-C3 2.37 124.86 116.472 B 441 FAD C4X-C4-N3 -2.33 120.24 123.432 D 441 FAD C4X-C4-N3 -2.33 120.25 123.432 C 441 FAD C4A-C5A-N7A -2.31 107.00 109.402 F 441 FAD C4X-C4-N3 -2.30 120.29 123.434 B 600 LMT C1B-O1B-C4' -2.29 112.29 117.962 A 441 FAD C1'-N10-C9A 2.27 120.08 118.294 A 600 LMT C1B-O1B-C4' -2.25 112.40 117.962 A 441 FAD O4B-C1B-C2B -2.24 103.66 106.932 D 441 FAD C9A-N10-C10 -2.24 118.98 121.913 D 500 DCQ C3M-O3-C3 2.19 124.22 116.473 A 500 DCQ C1M-C1-C6 -2.14 120.91 124.402 E 441 FAD C9A-N10-C10 -2.13 119.12 121.913 C 500 DCQ C1M-C1-C6 -2.12 120.94 124.402 C 441 FAD C9A-N10-C10 -2.12 119.14 121.912 D 441 FAD P-O3P-PA -2.11 125.57 132.833 F 500 DCQ C16-C15-C14 -2.03 98.02 113.422 F 441 FAD C9A-N10-C10 -2.02 119.26 121.914 D 600 LMT C1B-O1B-C4' -2.02 112.97 117.962 F 441 FAD P-O3P-PA -2.00 125.96 132.83


All (127) torsion outliers are listed below:

Mol Chain Res Type Atoms2 F 441 FAD O4B-C4B-C5B-O5B4 A 600 LMT C2-C1-O1'-C1'4 B 600 LMT C2'-C1'-O1'-C16 C 800 PS9 S2-S3-S4-S5




Mol Chain Res Type Atoms3 B 500 DCQ C5-C6-C7-C83 B 500 DCQ C1-C6-C7-C84 C 600 LMT O5'-C1'-O1'-C14 C 600 LMT C2-C1-O1'-C1'4 F 600 LMT C2-C1-O1'-C1'4 C 600 LMT C3'-C4'-O1B-C1B3 F 500 DCQ C6-C7-C8-C94 E 600 LMT C4'-C5'-C6'-O6'4 F 600 LMT C2B-C1B-O1B-C4'4 B 600 LMT O5B-C5B-C6B-O6B4 A 600 LMT O5'-C5'-C6'-O6'4 E 600 LMT O5'-C5'-C6'-O6'4 A 600 LMT C4'-C5'-C6'-O6'2 F 441 FAD C3B-C4B-C5B-O5B4 B 600 LMT O5'-C1'-O1'-C14 F 600 LMT O5B-C1B-O1B-C4'4 E 600 LMT O5B-C5B-C6B-O6B3 A 500 DCQ C6-C7-C8-C94 B 600 LMT O1'-C1-C2-C34 B 600 LMT C4B-C5B-C6B-O6B4 C 600 LMT O1'-C1-C2-C34 F 600 LMT C4'-C5'-C6'-O6'4 D 600 LMT O1'-C1-C2-C34 D 600 LMT C11-C10-C9-C84 C 600 LMT C7-C8-C9-C103 A 500 DCQ C11-C10-C9-C83 D 500 DCQ C10-C11-C12-C134 B 600 LMT C6-C7-C8-C94 A 600 LMT C11-C10-C9-C84 F 600 LMT C5-C6-C7-C84 A 600 LMT C5-C6-C7-C84 C 600 LMT C11-C10-C9-C83 F 500 DCQ C7-C8-C9-C104 B 600 LMT C11-C10-C9-C84 D 600 LMT C2'-C1'-O1'-C13 A 500 DCQ C7-C8-C9-C104 D 600 LMT C2-C3-C4-C54 E 600 LMT C5'-C4'-O1B-C1B4 E 600 LMT O1'-C1-C2-C33 F 500 DCQ C11-C12-C13-C143 C 500 DCQ C12-C13-C14-C153 A 500 DCQ C10-C11-C12-C13




Mol Chain Res Type Atoms3 D 500 DCQ C11-C10-C9-C84 C 600 LMT C4'-C5'-C6'-O6'4 C 600 LMT C2-C3-C4-C54 F 600 LMT C11-C10-C9-C83 B 500 DCQ C6-C7-C8-C94 C 600 LMT C4-C5-C6-C74 F 600 LMT C7-C8-C9-C103 C 500 DCQ C11-C12-C13-C143 B 500 DCQ C12-C13-C14-C154 E 600 LMT C1-C2-C3-C44 E 600 LMT C3'-C4'-O1B-C1B2 D 441 FAD C2'-C3'-C4'-O4'4 E 600 LMT C4-C5-C6-C74 D 600 LMT C7-C8-C9-C103 A 500 DCQ C9-C10-C11-C123 D 500 DCQ C11-C12-C13-C144 D 600 LMT C4-C5-C6-C74 F 600 LMT C2-C3-C4-C54 A 600 LMT C6-C7-C8-C94 D 600 LMT O5'-C1'-O1'-C14 C 600 LMT C2'-C1'-O1'-C14 E 600 LMT C2-C3-C4-C53 C 500 DCQ C11-C10-C9-C84 D 600 LMT C6-C7-C8-C94 D 600 LMT C1-C2-C3-C44 F 600 LMT O5B-C5B-C6B-O6B4 B 600 LMT C3-C4-C5-C63 E 500 DCQ C13-C14-C15-C163 B 500 DCQ C11-C12-C13-C144 B 600 LMT C9-C10-C11-C124 E 600 LMT C9-C10-C11-C124 E 600 LMT C4B-C5B-C6B-O6B3 D 500 DCQ C13-C14-C15-C164 C 600 LMT O5'-C5'-C6'-O6'4 B 600 LMT C1-C2-C3-C43 B 500 DCQ C13-C14-C15-C164 F 600 LMT O5'-C5'-C6'-O6'2 D 441 FAD C2'-C3'-C4'-C5'3 E 500 DCQ C7-C8-C9-C103 C 500 DCQ C9-C10-C11-C123 C 500 DCQ C10-C11-C12-C132 E 441 FAD PA-O3P-P-O5'




Mol Chain Res Type Atoms4 D 600 LMT C3-C4-C5-C64 A 600 LMT C2-C3-C4-C52 D 441 FAD O3'-C3'-C4'-O4'2 C 441 FAD C2'-C3'-C4'-O4'3 D 500 DCQ C12-C13-C14-C154 E 600 LMT C2'-C1'-O1'-C12 F 441 FAD C2'-C3'-C4'-C5'4 F 600 LMT C6-C7-C8-C93 F 500 DCQ C5-C4-O4-C4M4 E 600 LMT C7-C8-C9-C103 B 500 DCQ C5-C4-O4-C4M4 E 600 LMT C3-C4-C5-C63 C 500 DCQ C6-C7-C8-C93 F 500 DCQ C11-C10-C9-C84 E 600 LMT O5'-C1'-O1'-C14 E 600 LMT C11-C10-C9-C83 F 500 DCQ C3-C4-O4-C4M3 F 500 DCQ C9-C10-C11-C124 E 600 LMT C6-C7-C8-C92 C 441 FAD O3'-C3'-C4'-O4'4 E 600 LMT C5-C6-C7-C82 B 441 FAD O4B-C4B-C5B-O5B4 A 600 LMT C9-C10-C11-C122 F 441 FAD C2'-C3'-C4'-O4'3 B 500 DCQ C11-C10-C9-C83 B 500 DCQ C9-C10-C11-C122 C 441 FAD O4B-C4B-C5B-O5B3 C 500 DCQ C13-C14-C15-C163 B 500 DCQ C10-C11-C12-C132 E 441 FAD O4B-C4B-C5B-O5B4 C 600 LMT C3-C4-C5-C64 C 600 LMT C9-C10-C11-C122 E 441 FAD O3'-C3'-C4'-O4'2 D 441 FAD O3'-C3'-C4'-C5'3 B 500 DCQ C3-C4-O4-C4M2 D 441 FAD O4B-C4B-C5B-O5B2 A 441 FAD O4B-C4B-C5B-O5B3 E 500 DCQ C12-C13-C14-C153 D 500 DCQ C7-C8-C9-C10

There are no ring outliers.

26 monomers are involved in 125 short contacts:


Mol Chain Res Type Clashes Symm-Clashes3 C 500 DCQ 32 03 D 500 DCQ 34 03 F 500 DCQ 19 02 F 441 FAD 7 04 A 600 LMT 2 07 F 434 SO4 3 06 F 800 PS9 2 06 A 800 PS9 2 04 B 600 LMT 6 04 F 600 LMT 6 07 C 431 SO4 1 02 D 441 FAD 6 07 E 434 SO4 1 07 C 434 SO4 3 02 A 441 FAD 2 03 E 500 DCQ 18 07 C 432 SO4 1 07 F 431 SO4 1 06 E 800 PS9 2 04 D 600 LMT 1 03 B 500 DCQ 23 04 C 600 LMT 5 04 E 600 LMT 4 06 C 800 PS9 2 06 D 800 PS9 3 03 A 500 DCQ 16 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identi�ed as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identi�ed by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identi�ed rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not �nd su�cientequivalents in the CSD to analyse the geometry.


Ligand DCQ C 500

Bond lengths Bond angles

Torsions Rings

Ligand DCQ D 500


Torsions Rings

Ligand DCQ F 500


Torsions Rings


Ligand FAD F 441


Torsions Rings

Ligand LMT A 600


Torsions Rings


Ligand PS9 F 800


Torsions Rings


Ligand PS9 A 800


Torsions Rings


Ligand LMT B 600


Torsions Rings

Ligand LMT F 600


Torsions Rings


Ligand PS9 B 802 (B)


Torsions Rings


Ligand FAD D 441


Torsions Rings


Ligand PS9 B 802 (A)


Torsions Rings


Ligand FAD A 441


Torsions Rings


Ligand FAD C 441


Torsions Rings

Ligand DCQ E 500


Torsions Rings


Ligand PS9 E 800


Torsions Rings


Ligand LMT D 600


Torsions Rings

Ligand DCQ B 500


Torsions Rings

Ligand LMT C 600


Torsions Rings


Ligand FAD B 441


Torsions Rings

Ligand LMT E 600


Torsions Rings


Ligand PS9 C 800


Torsions Rings


Ligand PS9 D 800


Torsions Rings


Ligand FAD E 441


Torsions Rings

Ligand DCQ A 500


Torsions Rings

5.7 Other polymers iO

There are no such residues in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#nonstandard_residues_and_ligands


5.8 Polymer linkage issues iO

There are no chain breaks in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#polymer_linkage


6 Fit of model and data iO

6.1 Protein, DNA and RNA chains iO

In the following table, the column labelled `#RSRZ> 2' contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled `Q< 0.9' lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.

Mol Chain Analysed #RSRZ>2 OWAB(Å2) Q



Mol Chain Res Type RSRZ1 B 91 GLN 3.41 A 236 LEU 3.41 E 27 ASP 3.31 B 239 ASN 3.31 E 2 ALA 3.31 E 336 PRO 3.21 B 2 ALA 3.21 F 91 GLN 3.21 D 380 TYR 3.21 D 29 LYS 3.11 D 229 ASP 3.11 D 2 ALA 3.11 D 303 LYS 3.11 D 142 ASN 3.01 C 150 ALA 3.01 D 239 ASN 3.01 E 74 ILE 3.01 E 204 ARG 2.91 D 336 PRO 2.91 B 27 ASP 2.91 A 420 LYS 2.91 E 84 ASP 2.91 C 141 ALA 2.81 F 2 ALA 2.81 A 7 VAL 2.81 D 91 GLN 2.81 C 95 LYS 2.81 D 423 GLU 2.81 F 423 GLU 2.81 E 97 GLU 2.71 E 118 GLU 2.71 C 149 GLY 2.71 E 236 LEU 2.71 D 93 GLY 2.61 A 229 ASP 2.61 D 141 ALA 2.61 F 97 GLU 2.61 D 228 PRO 2.61 F 134 LYS 2.51 F 92 SER 2.51 D 334 ASN 2.51 B 343 LEU 2.5




Mol Chain Res Type RSRZ1 C 343 LEU 2.51 D 271 ALA 2.51 E 237 ASN 2.51 C 67 PRO 2.51 D 175 GLY 2.51 E 228 PRO 2.41 C 91 GLN 2.41 C 250 PHE 2.41 E 114 GLU 2.41 E 265 ASP 2.41 B 7 VAL 2.41 D 95 LYS 2.41 A 143 PRO 2.41 C 103 ILE 2.41 B 423 GLU 2.41 F 258 GLU 2.41 B 141 ALA 2.41 C 92 SER 2.41 A 142 ASN 2.31 C 114 GLU 2.31 E 353 GLU 2.31 B 303 LYS 2.31 A 353 GLU 2.31 A 15 ILE 2.31 C 142 ASN 2.31 E 94 LYS 2.31 F 376 LYS 2.31 E 141 ALA 2.31 A 173 LYS 2.31 D 112 GLY 2.31 E 240 THR 2.31 C 270 PRO 2.21 D 92 SER 2.21 A 27 ASP 2.21 D 178 TYR 2.21 A 381 PHE 2.21 E 303 LYS 2.21 F 265 ASP 2.21 A 138 GLU 2.21 D 97 GLU 2.21 A 32 LEU 2.21 B 381 PHE 2.2




Mol Chain Res Type RSRZ1 D 240 THR 2.21 D 118 GLU 2.21 E 227 GLU 2.21 A 41 PHE 2.21 D 420 LYS 2.21 A 8 ILE 2.11 D 117 GLU 2.11 E 258 GLU 2.11 D 270 PRO 2.11 E 173 LYS 2.11 A 348 ILE 2.11 C 381 PHE 2.11 D 8 ILE 2.11 C 79 GLU 2.11 C 131 GLU 2.11 C 164 ALA 2.11 B 41 PHE 2.11 C 29 LYS 2.11 A 92 SER 2.01 F 56 GLU 2.01 C 246 LYS 2.01 D 285 THR 2.01 C 118 GLU 2.01 A 204 ARG 2.01 F 171 LEU 2.01 C 163 PHE 2.01 F 72 GLU 2.01 F 114 GLU 2.01 C 151 ILE 2.01 E 87 THR 2.01 B 5 VAL 2.01 C 363 VAL 2.01 D 230 LYS 2.01 E 93 GLY 2.0

6.2 Non-standard residues in protein, DNA, RNA chains iO

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber de�ned in the chemical component dictionary. The B-factors column lists the minimum,median, 95th percentile and maximum values of B factors of atoms in the group. The columnlabelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_nonstandard_and_ligands


Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q



Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q 250 and outliersas shown on the geometry validation Tables will also be included. Each �t is shown from di�erentorientation to approximate a three-dimensional view.

Electron density around LMT C 600:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)


Electron density around LMT A 600:




Electron density around LMT F 600:





Electron density around LMT E 600:




Electron density around LMT B 600:





Electron density around PS9 D 800:





Electron density around PS9 E 800:





Electron density around LMT D 600:





Electron density around PS9 C 800:





Electron density around PS9 A 800:





Electron density around PS9 B 802 (A):




Electron density around PS9 B 802 (B):





Electron density around PS9 D 802:





Electron density around DCQ D 500:




Electron density around DCQ F 500:





Electron density around DCQ A 500:





Electron density around PS9 F 800:





Electron density around DCQ E 500:




Electron density around DCQ B 500:





Electron density around DCQ C 500:




Electron density around FAD E 441:





Electron density around FAD C 441:




Electron density around FAD F 441:





Electron density around FAD B 441:




Electron density around FAD A 441:





Electron density around FAD D 441:




6.5 Other polymers iO

There are no such residues in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_nonstandard_and_ligands

Overall quality at a glanceEntry compositionResidue-property plotsData and refinement statisticsModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA

Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues

Fit of model and data i Protein, DNA and RNA chains i Non-standard residues in protein, DNA, RNA chains i Carbohydrates i Ligands i Other polymers i

full wwpdb x-ray structure validation report i · • molecule 4 is dodecyl-beta-d-maltoside...

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